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MCL coexpression mm9:527: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.686627,0.204219,0.716126,0.123731,0.269875,0.346405,0.51055,0.536572,0.646925,0.308886,0.892635,0.237599,1.67598,0.134875,0,0.530547,0.377686,0.215337,0.751449,0.176628,0.329508,0.356242,0.122718,1.13761,0.381085,1.19145,0.287195,0.915208,0.611262,2.12625,0.624931,0.752328,0.176308,0.135203,0.155394,0.111136,0.332941,0.097604,0.276416,0.384293,0.76591,0.0536251,0.136236,1.56054,0.24907,0.457618,0.812613,0.0394476,0.474834,0.514446,0.404841,0.584697,0.759566,0.776306,1.69768,0.950326,2.37397,0.190698,0.36147,0.606104,1.06252,0.569343,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,2.50058,0.189925,0.899779,0.0145353,0.808562,0.0481979,5.15468,1.08401,1.13643,0.590017,1.61198,0.904727,3.39998,0.411949,2.35224,0.69807,5.83945,0.290012,0.145915,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.315787,0.287636,0.0656861,0.639644,0.457849,0.0288834,0.358446,0.624668,0.742871,0.514993,1.27935,1.39895,0.569344,0.296997,1.03226,0.526725,0.62491,0.744577,4.75728,1.5213,0.982794,0.381263,1.09124,0.26114,0.53175,0.714691,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.252176,0.877862,0.375176,1.0039,1.15925,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.766765,0.460443,1.73788,0.232952,0.394117,2.38709,0.500318,0.761071,0.29706,0.374365,0.839715,1.04618,0.866018,0.222538,0.230865,0.96517,0.697256,0.593895,1.16538,0.50503,0.367885,1.18797,0.33468,1.31116
|tfbs_overrepresentation_jaspar=MA0003.1;0.934438,MA0004.1;0.258473,MA0006.1;0.1319,MA0007.1;1.27649,MA0009.1;0.649874,MA0014.1;0.546364,MA0017.1;0.150118,MA0019.1;0.480432,MA0024.1;9.10405,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.430035,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.121113,MA0050.1;1.43876,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.0206669,MA0056.1;0,MA0057.1;0.0252827,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;2.02744,MA0061.1;0.0995825,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;1.17375,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;0.405789,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;1.59032,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;1.5822,MA0101.1;0.199903,MA0103.1;0.157724,MA0105.1;0.170132,MA0106.1;1.08833,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.679612,MA0113.1;0.400008,MA0114.1;0.0981613,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.231431,MA0140.1;0.330266,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;1.64479,MA0145.1;0.189432,MA0146.1;1.84184,MA0147.1;0.349075,MA0148.1;0.271704,MA0149.1;0.204102,MA0062.2;0.177386,MA0035.2;0.33429,MA0039.2;4.39345,MA0138.2;0.469076,MA0002.2;1.82632,MA0137.2;0.97737,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.370361,MA0065.2;1.68777,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.0285118,MA0155.1;2.32015,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.767982,MA0163.1;0.319589,MA0164.1;0.357779,MA0080.2;0.153997,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;1.27641,MA0102.2;1.35579,MA0258.1;0.301988,MA0259.1;0.101001,MA0442.1;0
}}

Latest revision as of 15:27, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:44333836..44333845,+p11@Rnf145
Mm9::chr2:49585812..49585827,-p@chr2:49585812..49585827
-
Mm9::chr4:135728233..135728238,-p@chr4:135728233..135728238
-
Mm9::chr4:135728282..135728310,+p4@E2f2
Mm9::chr5:89194174..89194185,+p3@Dck
Mm9::chr5:89194194..89194216,+p1@Dck
Mm9::chr5:89194217..89194224,+p5@Dck
Mm9::chr5:89194225..89194236,+p4@Dck
Mm9::chr5:89194237..89194248,+p2@Dck
Mm9::chr5:89194874..89194877,+p@chr5:89194874..89194877
+
Mm9::chr7:106976854..106976894,-p1@Neu3
Mm9::chr8:124471852..124471879,+p@chr8:124471852..124471879
+
Mm9::chr9:72286416..72286423,+p3@Mns1
Mm9::chr9:72286650..72286653,+p@chr9:72286650..72286653
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0004137deoxycytidine kinase activity0.0279406125020544
GO:0016997alpha-sialidase activity0.0419017343081136
GO:0019136deoxynucleoside kinase activity0.0465472798622322



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br><br><br>


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.934438
MA0004.10.258473
MA0006.10.1319
MA0007.11.27649
MA0009.10.649874
MA0014.10.546364
MA0017.10.150118
MA0019.10.480432
MA0024.19.10405
MA0025.10.873493
MA0027.12.275
MA0028.10.430035
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.121113
MA0050.11.43876
MA0051.10.388883
MA0052.10.669354
MA0055.10.0206669
MA0056.10
MA0057.10.0252827
MA0058.10.183941
MA0059.10.19314
MA0060.12.02744
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.11.17375
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.405789
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.11.59032
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.11.5822
MA0101.10.199903
MA0103.10.157724
MA0105.10.170132
MA0106.11.08833
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.10.679612
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.10.171891
MA0142.10.547747
MA0143.10.414534
MA0144.11.64479
MA0145.10.189432
MA0146.11.84184
MA0147.10.349075
MA0148.10.271704
MA0149.10.204102
MA0062.20.177386
MA0035.20.33429
MA0039.24.39345
MA0138.20.469076
MA0002.21.82632
MA0137.20.97737
MA0104.20.0740839
MA0047.20.380343
MA0112.20.370361
MA0065.21.68777
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.0285118
MA0155.12.32015
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.10.767982
MA0163.10.319589
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.21.27641
MA0102.21.35579
MA0258.10.301988
MA0259.10.101001
MA0442.10
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